Merge pull request #66 from KrishnaswamyLab/scipy-graph-shortest-path

Use `scipy.sparse.csgraph.shortest_path`

Author: scottgigante

.coveragerc

@@ -15,5 +15,3 @@ exclude_lines =
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.
-
-

.github/workflows/pre-commit.yml

@@ -0,0 +1,62 @@
+name: pre-commit
+on:
+  push:
+    branches-ignore:
+      - 'master'
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    if: >-
+      !endsWith(github.event.head_commit.message, '# ci skip') &&
+      (
+        startsWith(github.ref, 'refs/heads') ||
+        github.event.pull_request.draft == false
+      )
+
+    steps:
+
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Cache pre-commit
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}-
+
+      - name: Run pre-commit
+        id: precommit
+        uses: pre-commit/[email protected]
+        continue-on-error: true
+
+      - name: Commit files
+        if: steps.precommit.outcome == 'failure' && startsWith(github.ref, 'refs/heads')
+        run: |
+          if [[ `git status --porcelain --untracked-files=no` ]]; then
+            git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git add .
+            git checkout -- .github/workflows
+            git commit -m "pre-commit" -a
+          fi
+        shell: bash -ex {0}
+
+      - name: Push changes
+        if: steps.precommit.outcome == 'failure' && startsWith(github.ref, 'refs/heads')
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}
+
+      - name: Check pre-commit
+        if: steps.precommit.outcome == 'failure'
+        uses: pre-commit/[email protected]

.github/workflows/run_tests.yml

@@ -0,0 +1,77 @@
+name: Unit Tests
+
+on:
+  push:
+    branches-ignore:
+      - 'test_deploy'
+  pull_request:
+    branches:
+      - '*'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  run_tester:
+    runs-on: ${{ matrix.config.os }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {name: '3.10', os: ubuntu-latest, python: '3.10' }
+        - {name: '3.9', os: ubuntu-latest, python: '3.9' }
+        - {name: '3.8', os: ubuntu-latest, python: '3.8' }
+        - {name: '3.7', os: ubuntu-latest, python: '3.7' }
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Install system dependencies
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -y libhdf5-dev libhdf5-serial-dev pandoc gfortran libblas-dev liblapack-dev llvm-dev
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.config.python }}
+
+    - name: Cache Python packages
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{runner.os}}-${{ matrix.config.python }}-pip-${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
+        restore-keys: ${{runner.os}}-${{ matrix.config.python }}-pip-${{ env.pythonLocation }}-
+
+    - name: Install package & dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -U wheel setuptools
+        pip install -U .[test]
+        python -c "import graphtools"
+
+    - name: Run tests
+      run: |
+        nose2 -vvv
+
+    - name: Coveralls
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_SERVICE_NAME: github
+      run: |
+        coveralls
+
+    - name: Upload check results on fail
+      if: failure()
+      uses: actions/upload-artifact@master
+      with:
+        name: ${{ matrix.config.name }}_results
+        path: check

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: \.(ai|gz)$
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.6.4
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args: ['--target-version=py36']
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v1.5.4
+    hooks:
+      - id: autopep8
+#   - repo: https://gitlab.com/pycqa/flake8
+#     rev: 3.8.4
+#     hooks:
+#       - id: flake8
+#         additional_dependencies: ['hacking']

.travis.yml

@@ -8,9 +8,9 @@ graphtools
 .. image:: https://anaconda.org/conda-forge/graphtools/badges/version.svg
     :target: https://anaconda.org/conda-forge/graphtools/
     :alt: Latest Conda version
-.. image:: https://api.travis-ci.com/KrishnaswamyLab/graphtools.svg?branch=master
+.. image:: https://img.shields.io/github/workflow/status/KrishnaswamyLab/graphtools/Unit%20Tests/master?label=Github%20Actions
     :target: https://travis-ci.com/KrishnaswamyLab/graphtools
-    :alt: Travis CI Build
+    :alt: Github Actions Build
 .. image:: https://img.shields.io/readthedocs/graphtools.svg
     :target: https://graphtools.readthedocs.io/
     :alt: Read the Docs

README.rst

@@ -11,4 +11,3 @@ for file in \$files; do
 done
 EOF
 chmod +x .git/hooks/pre-commit
-

autoblack.sh

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/Makefile

@@ -1,2 +1,4 @@
-from .api import Graph, from_igraph, read_pickle
+from .api import from_igraph
+from .api import Graph
+from .api import read_pickle
 from .version import __version__

graphtools/__init__.py

@@ -1,11 +1,12 @@
-import numpy as np
-import warnings
+from . import base
+from . import graphs
 from scipy import sparse
+
+import numpy as np
 import pickle
 import pygsp
 import tasklogger
-
-from . import base, graphs
+import warnings
 
 _logger = tasklogger.get_tasklogger("graphtools")
 
@@ -36,7 +37,7 @@ def Graph(
     graphtype="auto",
     use_pygsp=False,
     initialize=True,
-    **kwargs
+    **kwargs,
 ):
     """Create a graph built on data.
 
@@ -255,7 +256,7 @@ def Graph(
         else:
             msg = msg + " and PyGSP inheritance"
 
-    _logger.debug(msg)
+    _logger.log_debug(msg)
 
     class_names = [p.__name__.replace("Graph", "") for p in parent_classes]
     try:
@@ -273,7 +274,7 @@ def Graph(
                 pass
 
     # build graph and return
-    _logger.debug(
+    _logger.log_debug(
         "Initializing {} with arguments {}".format(
             parent_classes,
             ", ".join(